Apr 07, 2021
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Windows
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MMB is a multiresolution modeling tool for building 3D structural and dynamical models of macromolecules. It gives you explicit control over the degrees of freedom, forces, constraints, and molecules in your system.
MMB 3.4 for Windows
This builds on the earlier release in which Emanuel Peter and Jiri Cerny implemented their Nucleotide Conformers (NtC's) and includes updated parameters.
Since version 2.19 MMB reads triclinic density maps. In 3.0, we introduced the Planck's-Law noise generator.
Thanks to Michal Tykac, MMB can now read MRC density maps. It can also read and write mmCIF structure files (not just PDB).
There are some undocumented features to help fit DNA in icosohedral viruses, contact us if you work on that.
For simple nucleic acid folding problems, you should try our easy to use server at webmmb.datmos.org .
If you are a Linux or Mac user, we remind you that Docker images are available for trunk and several named releases on dockerhub: samuelflores/mmb-ubuntu . Install docker ( https://docs.docker.com/install/linux/docker-ce/ubuntu/ ) and then issue: docker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:3.0 Or if you like living on the edge: docker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:latest This mounts your current directory in the docker container. You can have your input files in the image's /work directory, and also write output persistently. Note "latest" is bleeding-edge code. The up to date source code is at: https://github.com/samuelflores/MMB.
3.4
Apr 07, 2021
MMB recent releases
In the 2.18 release, Emanuel Peter, Bohdan Schneider, and Jiri Cerny implemented their Nucleotide Conformers (NtC's). These improve the conformational parameters of consecutive bases, for instance to form double helices. Version 2.19 has the difference that it reads triclinic density maps. In 3.0, we introduced the Planck's-Law noise generator. Lastly, we slightly updated NtC parameters.
Binaries are provided below. But you might prefer a docker container which runs MMB 3.0 like a dream. Install docker ( https://docs.docker.com/install/linux/docker-ce/ubuntu/ ) and then issue:
docker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:3.0
Or if you like living on the edge:
docker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:latest
This mounts your current directory in the docker container. You can have your input files in there, and also write output persistently. Note "latest" is bleeding-edge code.
Lastly, we have moved from subversion to git. The up to date code is at:
https://github.com/samuelflores/MMB
MMB 2.18
Nov 30, 2018
In this release, Emanuel Peter, Bohdan Schneider, and Jiri Cerny implemented their Nucleotide Conformers (NtC's). These improve the conformational parameters of consecutive bases, for instance to form double helices. View License
(old) MMB 2.10
In this release, reading in PDB files and generating internal coordinate models based on them, is MUCH faster. matchFast now works even with normal-precision, standard PDB files, and is in fact the only matching method permitted. The accuracy and speed issues associated with coordinate matching in earlier releases are now solidly addressed. Unfortunately MMB no longer guesses missing backbone atom information.
A couple of bugs which may have affected 2.9.2 users have been fixed. The scrubber didn't always behave properly -- I fixed this and also removed the setForceAndStericScrubber parameter .. see the ref guide for details. The applyContactsWithin was also not working properly, and has also been fixed -- also this command now appears in the ref guide, whereas before it was effectively secret. Lastly, there was some code reorganization that doesn't affect the user, just the maintainability.
This is a binary release. Just download the appropriate package and unzip into an appropriate folder. You will find a tutorial guide in the package with instructions for setting your path (needed for Mac and Linux). Run exercise 0 from the same tutorial to make sure everything is working.
MMB 2.10
Aug 14, 2012
PLEASE CITE THESE PAPERS
Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman (2010) RNA 16(9): 1769-78. (2010)
(old) MMB 2.11
MMB release 2.11.
There is a Cent0S version 5 release compiled by Shaq Liu available upon request (but it's not completely up to date)
MMB 2.11
Jan 16, 2013
MMB 2.11 View License
PLEASE CITE THESE PAPERS
Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman (2010) RNA 16(9): 1769-78. (2010)
(old) MMB 2.12
In this release, we introduce long chain IDs, making memory the only limitation on number of molecules. We also fix a bug with the setHelicalStacking feature, though no one seems to have noticed that existed.
MMB 2.12
Apr 23, 2013
MMB 2.12 View License
(old) MMB 2.13
This release is mostly about "Physics where you want it," which allows you to turn on the PARM99 force field for specified residues in your system. This is still a little known feature, but features in upcoming papers and will probably become more widely used. There were a couple of bugs in release 2.12 which have been fixed in this release. First, the includeNonBondAtomsInResidues command was including all atoms in the system rather than just those in the specified residues; as a result simulations ran very slowly. In some cases bonded forces were being turned off, which led to odd ring-opening behavior in nucleic acids, proline, etc. There are also some changes that have been made one layer deeper, in MolModel. Whereas the tryptophan aromatic group chain was intended to be rigid, the wrong bond was being treated as a ring closing bond, causing odd out-of-plane motions. All the mentioned problems have been fixed. Even if the above issues didn't cause you a problem before, you will notice "Physics where you want it" runs much faster now. Also I've changed the N-CA bond in proline from rigid to torsion -- though this was more a matter of taste.
There is also a new example, using ICFF to fit Ribose Binding Protein into a density map. A few months from now, we hope to release our MMB GUI -- stay tuned!
MMB 2.13
Aug 27, 2013
PLEASE CITE THESE PAPERS
Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman; Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R.; Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman; Proceedings of the Pacific Symposium on Biocomputing. (2010)
Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman; RNA 16(9): 1769-78. (2010)
(old) MMB 2.14
In release 2.14 I improved a few features and added several others.
First, Physics where you want it was not including any monoAtoms. Now all atoms created with this command are automatically added to the physics zone. You can read in ion positions from a PDB file also, you just need to be careful about atom and residue names in that file. For example, the atom name for the magnesium ion should be Mg+2, and its residue name should be MG.
I have introduced a new residue type, a disulphide bridging cysteine. You can specify it using the single letter code ‘X’. You can also infer it from the input PDB file, if you name the residue in that file CYX, rather than CYS (the latter will be interpreted as a normal, non-bridged cysteine). Thus it is compatible with both the protein and loadSequencesFromPdb commands. To actually bridge the sulphurs, you would use the new addRingClosingBond command. An example of this is supplied, see the new commands.disulphide-bonded-cysteines.dat . There is a new figure to explain this, in the Mobilizers and constraints chapter; the usage is explained in the Forces chapter.
There were some silly limitations to how one could mix user defined variables, numbers, and +/- operators, which have now been removed. You can now mix these more or less as you wish, though absolute residue numbers still have to be leftmost in the expression. You can also use a leading ‘- ‘ in a residue number, and this will correctly be interpreted as part of the residue number rather than an operator.
Have you ever simply wanted to impose a certain secondary structure in a certain region of your model? Say, make a helix-turn-helix into a single continuous helix? Well, with the new setPhiPsiAngles command you can do just that. It sets the phi, psi, and peptide dihedral angles to the defaults for Alpha, ParallelBeta and AntiParallelBeta secondary structures, overriding whatever values these dihedrals may have taken from the input structure file.
The new psiPhiMobility command is used for specifying the bond mobility for the bonds connecting the N to CA, and the CA to C on the protein backbone, for a given stretch of residues. It is equivalent to issuing the singleBondMobility command for the two mentioned bonds, for each residue in the range.
Quite importantly, we have brought back the matchGapped macro. When issued, it sets guessCoordinates to True, meaning that if you have missing atoms or even entire residues in your input PDB file, it will guess positions for the missing atoms, and still perfectly match the remaining (non-missing) atoms. Even the default matchFast behavior guesses side chain positions, but with matchGapped you can leave out backbone atoms. You will probably get back bond geometries at the boundary between the known and missing backbone atoms, which you can correct using the singleBondMobility .. Free command.
We also have improved the mobilizeInterfaces command, which lets you set the bond mobility for residues at a certain interface. Firstly, it now bases the definition of “interface” on all atoms, not just Cα and C3* atoms. Secondly, it is now much more economical. Lastly, you can define the interface differently .. specifying one or more chains that form a complex, and then asking for all interfaces with other chains.
Lastly, we have a new method of adding residues to the physics zone. Just set the new parameter physicsRadius to some value greater than zero. It will look for all “flexible” atoms – defined as atoms in a mobilizedBody of mass < 40, and then include all residues within physicsRadius of these, in the physics zone.
MMB 2.14
Dec 30, 2013
PLEASE CITE THESE PAPERS
Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman; RNA 16(9): 1769-78. (2010)
Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. Flores, SC. Nucleic acids research, 29 Sept. (2013)
Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman; Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman; Proceedings of the Pacific Symposium on Biocomputing. (2010)
(old) MMB 2.15 with GUI
This release includes the GUI plugin for Chimera.
A tutorial is available.
MMB 2.15
Nov 09, 2014
PLEASE CITE THESE PAPERS
MMB-GUI: multiscale simulation of conformational changes in large macromolecular complexesAlex Tek, Andrei A. Korostelev, and Samuel Coulbourn Flores(submitted) (2014)
(old) MMB 2.16.5 with GUI
MMB has been branched, some of the newest features in the underlying code are only available in a non-GUI version. Thus this one is a little behind but does have the Chimera GUI.
MMB 2.16.5 with GUI for OSX
Jan 01, 2016
MMB with Chimera GUI for OSX. See tutorial for setup. View License
(old) MMB 2.16 with GUI
In release 2.16 I improved a few features and added several others. The densityForce command doesn’t work in the OSX version of MMB 2.15; this has been fixed in 2.16. The RNA threading example has been modernized and will give cleaner results.
The gappedThreading command previously aligned entire chains. You can still do this, but now there is a new option to align specified residue stretches. The default spring constant has also changed, to 30.0 kJ/mol/nm2 (was 3.0) for both threading and gappedThreading.
The loadSequencesFromPdb command has been improved, and is now compatible with long chain IDs.
A modification has been made to the U A HelicalStackingA3 / HelicalStackingA5 / Cis parameters in parameters.csv.
Command line feedback messages now show relative rather than absolute paths to code.
As of 2.15, we have a GUI in the form of a Chimera plugin. See the tutorial for a usage example.
MMB 2.16 for OSX 10.9
Jun 23, 2015
Built on Mavericks. View License
PLEASE CITE THESE PAPERS
Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. Flores, SC. Nucleic acids research, (2013)
Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman; Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman; Proceedings of the Pacific Symposium on Biocomputing. (2010)
Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman; RNA 16(9): 1769-78. (2010)
(old) MMB 2.17 WITHOUT GUI
This release adds a few useful features, such as progressive morphing and constraints for ions. However it does NOT include the GUI.
For linux, please be advised that the binaries may not run on a different Linux flavor than that on which they were compiled.
MMB 2.17 WITHOUT GUI
Jan 01, 2016
This release has the same binaries as 2.17. The library locations have been set with rpath, so you should be able to run it without setting your dynamically linked library path, though you might want to move your old libs to prevent possible conflicts. The bulk of the changes are to the tutorial, to get it more in sync with the rest of the distribution. I have also made numerous changes to the example command files. Your learning experience should be much improved. View License
(old) MMB 2.3.1 for Windows
This is a Windows-only release. It is very similar to 2.3. Some error messages have been improved, and some obsolete commands removed (but these were never in the reference guide to begin with).
This is not an installer. It is a compressed archive with a precompiled executable. Please decompress the archive in the location of your choice (we suggest C:usersMMB_Windows_2_3_1). Inside you will find a tutorial with further instructions.
MMB-Windows-2.3.1
May 02, 2011
(old) MMB 2.6
In this release, I've reduced the memory requirement of the density map reader, so it should run as fast on Mac as it does on Linux. The way the continuous derivative of the discrete density is taken, has been improved. Also, this revision supports DNA explicitly. As of 2.6.1, proteinThreading pulls together all corresponding protein atoms, not just backbone atoms.
MMB 2.6 binaries for Mac OSX Leopard and higher
Oct 20, 2011
This is a dynamically linked compilation. View License
PLEASE CITE THESE PAPERS
Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
Flores, S. & Altman, R. (2010). Turning limited experimental information into 3D models of RNA RNA 16, 1769-1778. (2010)
* Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
(old) MMB 2.8
In this latest release we enable reading the chain IDs, sequences, residue numbers, and insertion codes directly from the input structure file, for protein and RNA. These molecules can have gaps and insertion codes in the numbering. Other new commands and changes are explained in the reference guide.
MMB 2.8
Feb 09, 2012
PLEASE CITE THESE PAPERS
* Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman (2010) RNA 16(9): 1769-78. * Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing.Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 .Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
(old revision) MMB 2.3
MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, M 2.3 differs from RNABuilder 2.2 mostly internally. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient. Also in this release, some rarely used features have been removed, but these were never in the tutorial literature so their absence should go largely unnoticed. The default input file name is now commands.dat rather than contacts.dat. A couple of somewhat obscure bugs were fixed. The error messages are more informative, and more aggressively prevent the user from risky or incorrect construction of the input file. As you may have gathered, the user experience does not change much in this release.
M.2_3
Feb 05, 2011
PLEASE CITE THESE PAPERS
Samuel Coulbourn Flores, Russ B. Altman. Structural insights into Pre-Translocation Ribosome Motions. In Proceedings of Pacific Symposium on Biocomputing'2011. pp.205~216 (2011) View
Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
Turning limited experimental information intio 3D models of RNA, by Samuel C Flores and Russ B Altman, RNA 16(9):1769-78 (2010). (2010)
RNABuilder 2.0
This is the RNABuilder 2.0 binary release
RNABuilder 2.0
Jul 21, 2010
This contains executable, library, and example files for RNABuilder 2.0.Notes
PLEASE CITE THESE PAPERS
Samuel Flores and Russ Altman, "Turning limited experimental information into 3D models of RNA," RNA (accepted) (2010)
RNABuilder 2.2
RNABuilder 2.2 supports proteins and introduces the monoAtoms command for instantiating monatomic ions. The updated tutorial has two protein exercises, one for threading and one for morphing.
RNABuilder 2.2
Dec 23, 2010
PLEASE CITE THESE PAPERS
"Predicting RNA structure by multiple template homology modeling", Proceedings of the Pacific Symposium on Biocomputing (2010) 216-227 (2010)
Flores SC and Altman RB, "Turning limited experimental information into 3D models of RNA", RNA (2010) 16:1769-78 (2010)
